They had South Sudan in OTL and they weren't able to Arabize it, so they definitely wouldn't be able to Arabize the Great Lakes region. Even holding it is difficult, since the population density was very high, the Sudd is in the way, and they'd be conquering some very organised states.
Long-term the region would have rapid population growth as in OTL and almost certainly split from Egypt by then if it hasn't already. Assuming Europeans don't cleave it off Egypt before then, a distinct possibility.